Gene detail

Detailed information of OS493_030816-T1 in Lophelia pertusa

Genomic Location: scaffold_203:263339...268479
NR annotation: KAJ7353973.1, GTPase-activating protein S13 [Desmophyllum pertusum]
Species Lophelia pertusa · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

Transcript

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q3ZCC9	Protein SEC13 homolog OS=Bos taurus OX=9913 GN=SEC13 PE=2 SV=1
P55735	Protein SEC13 homolog OS=Homo sapiens OX=9606 GN=SEC13 PE=1 SV=3
Q9D1M0	Protein SEC13 homolog OS=Mus musculus OX=10090 GN=Sec13 PE=1 SV=3

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0004398 (this species only)

Pfam domain

No Pfam domain signature was detected for OS493_030816-T1. This gene does have a gene model — the search simply returned no hit.

InterPro

InterPro term	Type	Description	Source
IPR037363 all species →	Family	Sec13/Seh1 family	Interproscan
IPR036322 all species →	Homologous_superfamily	WD40-repeat-containing domain superfamily	Interproscan
IPR015943 all species →	Homologous_superfamily	WD40/YVTN repeat-like-containing domain superfamily	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11024 all species →	NUCLEAR PORE COMPLEX PROTEIN SEC13 / SEH1 FAMILY MEMBER	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0005198 all species →	Molecular Function	structural molecule activity	Interproscan
GO:0006606 all species →	Biological Process	protein import into nucleus	Interproscan
GO:0030127 all species →	Cellular Component	COPII vesicle coat	Interproscan
GO:0031080 all species →	Cellular Component	nuclear pore outer ring	Interproscan
GO:0032008 all species →	Biological Process	positive regulation of TOR signaling	Interproscan
GO:0032527 all species →	Biological Process	protein exit from endoplasmic reticulum	Interproscan
GO:0090114 all species →	Biological Process	COPII-coated vesicle budding	Interproscan
GO:0005515 all species →	Molecular Function	protein binding	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

No KEGG orthology assignment for OS493_030816-T1.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of OS493_030816-T1 across 110 RNA-seq samples of Lophelia pertusa. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

110Samples

110TPM > 0

7Conditions

103.4Max TPM

44.1Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
polyp at pH7 9	18	18	33.19	47.29
polyp at pH7 6	18	18	41.81	58.99
coral polyp · control treatment	16	16	53.43	85.06
coral polyp · oil and dispersant treatment	16	16	47.46	71.11
coral polyp · oil treatment	16	16	45.70	63.61
coral polyp · dispersant treatment	16	16	37.60	52.51
Polyp	10	10	55.20	103.45

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11359494	polyp at pH7 9	not recorded	not recorded	not recorded	-	47.29
SRR11359519	polyp at pH7 9	not recorded	not recorded	not recorded	-	40.74
SRR11359507	polyp at pH7 9	not recorded	not recorded	not recorded	-	38.99
SRR11359521	polyp at pH7 9	not recorded	not recorded	not recorded	-	37.24
SRR11359506	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.73
SRR11359496	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.29
SRR11359495	polyp at pH7 9	not recorded	not recorded	not recorded	-	36.08
SRR11359520	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.44
SRR11359518	polyp at pH7 9	not recorded	not recorded	not recorded	-	35.30
SRR11359523	polyp at pH7 9	not recorded	not recorded	not recorded	-	34.57
SRR11359522	polyp at pH7 9	not recorded	not recorded	not recorded	-	31.36
SRR11359497	polyp at pH7 9	not recorded	not recorded	not recorded	-	30.83
SRR11359509	polyp at pH7 9	not recorded	not recorded	not recorded	-	28.06
SRR11359508	polyp at pH7 9	not recorded	not recorded	not recorded	-	27.45
SRR11359499	polyp at pH7 9	not recorded	not recorded	not recorded	-	26.60
SRR11359510	polyp at pH7 9	not recorded	not recorded	not recorded	-	25.65
SRR11359498	polyp at pH7 9	not recorded	not recorded	not recorded	-	24.86
SRR11359511	polyp at pH7 9	not recorded	not recorded	not recorded	-	23.97
SRR11359505	polyp at pH7 6	not recorded	not recorded	not recorded	-	58.99
SRR11359501	polyp at pH7 6	not recorded	not recorded	not recorded	-	56.44
SRR11359525	polyp at pH7 6	not recorded	not recorded	not recorded	-	54.41
SRR11359500	polyp at pH7 6	not recorded	not recorded	not recorded	-	53.71
SRR11359504	polyp at pH7 6	not recorded	not recorded	not recorded	-	52.27
SRR11359512	polyp at pH7 6	not recorded	not recorded	not recorded	-	50.32
SRR11359517	polyp at pH7 6	not recorded	not recorded	not recorded	-	45.94
SRR11359516	polyp at pH7 6	not recorded	not recorded	not recorded	-	43.08
SRR11359528	polyp at pH7 6	not recorded	not recorded	not recorded	-	41.70
SRR11359524	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.70
SRR11359502	polyp at pH7 6	not recorded	not recorded	not recorded	-	36.41
SRR11359527	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.67
SRR11359526	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.67
SRR11359529	polyp at pH7 6	not recorded	not recorded	not recorded	-	34.12
SRR11359513	polyp at pH7 6	not recorded	not recorded	not recorded	-	31.74
SRR11359503	polyp at pH7 6	not recorded	not recorded	not recorded	-	30.82
SRR11359514	polyp at pH7 6	not recorded	not recorded	not recorded	-	29.90
SRR11359515	polyp at pH7 6	not recorded	not recorded	not recorded	-	26.73
SRR16705973	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	85.06
SRR16705965	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	68.77
SRR16705992	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.44
SRR16705990	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	66.08
SRR16705946	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	61.63
SRR16705974	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	58.67
SRR16705957	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	57.31
SRR16705971	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	56.82
SRR16705970	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	50.53
SRR16705989	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	47.21
SRR16705942	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	44.17
SRR16705972	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.99
SRR16705943	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	43.93
SRR16705991	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	36.28
SRR16705975	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	34.48
SRR16705960	coral polyp · control treatment	coral polyp	polyp	control treatment	SRP344271	33.53
SRR16705995	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	71.11
SRR16706005	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	66.03
SRR16705945	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	62.50
SRR16705993	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	60.55
SRR16705997	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	50.29
SRR16706004	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	49.47
SRR16705979	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	45.91
SRR16705977	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.82
SRR16705947	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	44.12
SRR16705982	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	41.79
SRR16705976	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.60
SRR16705996	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	39.33
SRR16705994	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.63
SRR16705944	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	38.43
SRR16705978	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	34.44
SRR16705948	coral polyp · oil and dispersant treatment	coral polyp	polyp	oil and dispersant treatment	SRP344271	32.38
SRR16705962	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	63.61
SRR16705981	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	61.95
SRR16705999	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	58.71
SRR16705983	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	57.48
SRR16705980	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	50.04
SRR16705984	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.41
SRR16705961	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	49.27
SRR16706000	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	48.08
SRR16705949	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	44.33
SRR16705952	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	43.44
SRR16705951	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	39.90
SRR16705950	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	37.13
SRR16705964	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	33.85
SRR16706001	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.74
SRR16705963	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	31.36
SRR16705998	coral polyp · oil treatment	coral polyp	polyp	oil treatment	SRP344271	30.97
SRR16705985	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	52.51
SRR16705958	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	46.82
SRR16705969	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.41
SRR16705959	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	45.14
SRR16705956	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.90
SRR16705986	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	44.17
SRR16705988	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	42.17
SRR16705966	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	40.04
SRR16705967	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.48
SRR16705987	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	35.22
SRR16705954	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.84
SRR16706003	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	32.46
SRR16705955	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.56
SRR16705953	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	31.31
SRR16705968	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	24.16
SRR16706002	coral polyp · dispersant treatment	coral polyp	polyp	dispersant treatment	SRP344271	17.47
SRR23025710	Polyp	not recorded	not recorded	not recorded	-	103.45
SRR23025712	Polyp	not recorded	not recorded	not recorded	-	97.06
SRR7746667	Polyp	not recorded	not recorded	not recorded	-	74.42
SRR23025713	Polyp	not recorded	not recorded	not recorded	-	62.64
SRR23025708	Polyp	not recorded	not recorded	not recorded	-	48.70
SRR23025711	Polyp	not recorded	not recorded	not recorded	-	47.78
SRR23025709	Polyp	not recorded	not recorded	not recorded	-	40.12
SRR7746668	Polyp	not recorded	not recorded	not recorded	-	33.92
SRR7746669	Polyp	not recorded	not recorded	not recorded	-	29.14
SRR7746666	Polyp	not recorded	not recorded	not recorded	-	14.80

Source: CnidoSite RNA-seq expression matrices (LPERT_TPM, StringTie quantification over 110 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.